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- PDB-7cyg: Crystal structure of a cysteine-pair mutant (Y113C-P190C) of a ba... -

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Basic information

Entry
Database: PDB / ID: 7cyg
TitleCrystal structure of a cysteine-pair mutant (Y113C-P190C) of a bacterial bile acid transporter before disulfide bond formation
ComponentsTransporter, sodium/bile acid symporter family
KeywordsTRANSPORT PROTEIN / Bile acid transporter / ASBT / NTCP / SLC10
Function / homologyBile acid:sodium symporter/arsenical resistance protein Acr3 / Bile acid:sodium symporter / Sodium Bile acid symporter family / Sodium/solute symporter superfamily / membrane / Ketopantoate/pantoate/pantothenate transporter PanS
Function and homology information
Biological speciesYersinia frederiksenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.198 Å
AuthorsWang, X. / Lyu, Y. / Ji, Y. / Sun, Z. / Zhou, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770783 China
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: An engineered disulfide bridge traps and validates an outward-facing conformation in a bile acid transporter.
Authors: Wang, X. / Lyu, Y. / Ji, Y. / Sun, Z. / Zhou, X.
History
DepositionSep 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transporter, sodium/bile acid symporter family
B: Transporter, sodium/bile acid symporter family


Theoretical massNumber of molelcules
Total (without water)65,3382
Polymers65,3382
Non-polymers00
Water00
1
A: Transporter, sodium/bile acid symporter family


Theoretical massNumber of molelcules
Total (without water)32,6691
Polymers32,6691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transporter, sodium/bile acid symporter family


Theoretical massNumber of molelcules
Total (without water)32,6691
Polymers32,6691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)189.605, 47.164, 70.681
Angle α, β, γ (deg.)90.000, 100.840, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 4 through 302)
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 4 - 302 / Label seq-ID: 4 - 302

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 4 through 302)AA
2chain BBB

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Components

#1: Protein Transporter, sodium/bile acid symporter family


Mass: 32669.088 Da / Num. of mol.: 2 / Mutation: Y113C, P190C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia frederiksenii (bacteria) / Gene: NCTC11470_02445 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A380PV03

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 4.7 / Details: 0.1 M Na+-phosphate/citrate pH 4.7, 36% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.198→45.72 Å / Num. obs: 9572 / % possible obs: 91.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 52.92 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.061 / Rrim(I) all: 0.124 / Net I/σ(I): 11 / Num. measured all: 37170
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.198-3.2543.90.37218634790.8790.210.4293.893.7
9.142-45.723.50.03916734780.9980.0240.04622.699.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.3data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N7W

4n7w


Resolution: 3.198→35.684 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3014 474 4.96 %
Rwork0.2626 9082 -
obs0.2646 9556 91.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.15 Å2 / Biso mean: 34.7569 Å2 / Biso min: 10.58 Å2
Refinement stepCycle: final / Resolution: 3.198→35.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4511 0 0 0 4511
Num. residues----605
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2718X-RAY DIFFRACTION1.957TORSIONAL
12B2718X-RAY DIFFRACTION1.957TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1984-3.66090.32861320.2702288288
3.6609-4.61070.29191620.2617284089
4.6107-35.6840.29861800.25963360100

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